rand_query_ES: Generate WTCS Null Distribution with Random Queries

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Generate WTCS Null Distribution with Random Queries

Description

Function computes null distribution of Weighted Connectivity Scores (WTCS) used by the LINCS GESS method for computing nominal P-values.

Usage

rand_query_ES(h5file, N_queries = 1000, dest, write = TRUE)

Arguments

h5file	character(1), path to the HDF5 file representing the reference database
N_queries	number of random queries
dest	path to the output file (e.g. "ES_NULL.txt")
write	Logical value indicating if results should be written to dest.

Value

File with path assigned to dest

References

Subramanian, A., Narayan, R., Corsello, S. M., Peck, D. D., Natoli, T. E., Lu, X., Golub, T. R. (2017). A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell, 171 (6), 1437-1452.e17. URL: https://doi.org/10.1016/j.cell.2017.10.049

See Also

gess_lincs

Examples

db_path = system.file("extdata", "sample_db.h5", package="signatureSearch")
rand <- rand_query_ES(h5file=db_path, N_queries=5, dest="ES_NULL.txt", write=FALSE)
unlink("ES_NULL.txt")

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.